BACKGROUND: The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope. To assess their overlap, we must know the correspondences between compounds, reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences. RESULTS: KEGG contains 179 module pathways versus 1,846 base pathways in MetaCyc; KEGG contains 237 map pathways versus 296 super pathways in MetaCyc. KEGG pathways contain 3.3 times as many reactions on average as do MetaCyc pathways, and the databases employ different conceptualizations of metabolic pathways. KEGG contains 8,692 reactions versus 10,262 for MetaCyc. 6,174 KEGG reactions are components of KEGG pathways versus 6,348 for MetaCyc. KEGG contains 16,586 compounds versus 11,991 for MetaCyc. 6,912 KEGG compounds act as substrates in KEGG reactions versus 8,891 for MetaCyc. MetaCyc contains a broader set of database attributes than does KEGG, such as relationships from a compound to enzymes that it regulates, identification of spontaneous reactions, and the expected taxonomic range of metabolic pathways. MetaCyc contains many pathways not found in KEGG, from plants, fungi, metazoa, and actinobacteria; KEGG contains pathways not found in MetaCyc, for xenobiotic degradation, glycan metabolism, and metabolism of terpenoids and polyketides. MetaCyc contains fewer unbalanced reactions, which facilitates metabolic modeling such as using flux-balance analysis. MetaCyc includes generic reactions that may be instantiated computationally. CONCLUSIONS: KEGG contains significantly more compounds than does MetaCyc, whereas MetaCyc contains significantly more reactions and pathways than does KEGG, in particular KEGG modules are quite incomplete. The number of reactions occurring in pathways in the two DBs are quite similar.

UNLABELLED: BioLingua is an interactive, web-based programming environment that enables biologists to analyze biological systems by combining knowledge and data through direct end-user programming. BioLingua embeds a mature symbolic programming language in a frame-based knowledge environment, integrating genomic and pathway knowledge about a class of similar organisms. The BioLingua language provides interfaces to numerous state-of-the-art bioinformatic tools, making these available as an integrated package through the novel use of web-based programmability and an integrated Wiki-based community code and data store. The pilot instantiation of BioLingua, which has been developed in collaboration with several cyanobacteriologists, integrates knowledge about a subset of cyanobacteria with the Gene Ontology, KEGG and BioCyc knowledge bases. We introduce the BioLingua concept, architecture and language, and give several examples of its use in complex analyses. AVAILABILITY: Extensive documentation is available online at http://nostoc.stanford.edu/Docs/index.html CONTACT: [email protected]

LiveWorld is a graphical environment designed to support research into programming with active objects. It offers novice users a world of manipulable objects, with graphical objects and elements of the programs that make them move integrated into a single framework. LiveWorld is designed to support a style of programming based on rule-like agents that allow objects to be responsive to their environment. In order to make this style of programming accessible to novices, computational objects such as behavioral rules need to be just as concrete and accessible as the graphic objects. LiveWorld fills this need by using a novel object system, Framer, in which the usual structures of an objectoriented system (classes, objects, and slots) are replaced with a single one, the frame, that has a simple and intuitive graphic representation. This unification enables the construction of an interface that achieves elegance, simplicity and power. Allowing graphic objects and internal computational obje...

Article Free Access Share on Two approaches to casual interaction over computer and video networks Authors: Alan Borning Rank Xerox EuroPARC, 61 Regent Street, Cambridge CB2 1AB, United Kingdom Rank Xerox EuroPARC, 61 Regent Street, Cambridge CB2 1AB, United KingdomView Profile , Michael Travers Rank Xerox EuroPARC, 61 Regent Street, Cambridge CB2 1AB, United Kingdom Rank Xerox EuroPARC, 61 Regent Street, Cambridge CB2 1AB, United KingdomView Profile Authors Info & Claims CHI '91: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsApril 1991 Pages 13–19https://doi.org/10.1145/108844.108847Published:01 March 1991Publication History 62citation667DownloadsMetricsTotal Citations62Total Downloads667Last 12 Months38Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF